How To Have Good Gut Flora and Why You Desperately Need It!

“I'd like to know more about gut flora and how to maintain good conditions related to flora in my gut. Regular physicians don't seem to know much about this area.” – Jay

Maintaining good gut flora is a huge topic and unbelievably important to your health.

In fact, if your gut flora isn’t functioning well, it’s no exaggeration to say that while it may not kill you, it could make you wish you were dead, because it will make your life hell.

So, Jay, thank you for sending in this question because it is something absolutely everyone needs to know about. I hope you find this article helpful.

In this blog post, I’m going to look at:

1) What is gut flora?

2) Why maintaining good gut flora is so important.

3) What interferes with healthy gut flora?

4) How to support gut flora so it fosters your health instead of making you sick. You CAN fix your flora!

1) What is gut flora?

Gut flora means all the micro-organisms in your digestive system. They include bacteria, protozoa, yeasts, fungus – there are at least 500 known types of microbes in the human gut (and no doubt more to be discovered by science.)

2) Why you need healthy, balanced gut flora:

Some of the microbes in your gut are beneficial and others are not. But as long as the good guys are healthy, they do an amazing job of keeping the bad ones (like Candida) under control.

In addition, they…

digest your food so that you can absorb the nutrients your body and brain need to function properly,

help to produce vitamins,

break down viruses and other pathogens that make you sick,

coat the inside of the digestive tract to protect it from invaders like parasites, undigested food, and toxins from foods, chemicals and heavy metals

suppress many carcinogenic substances

As you can see, healthy gut flora is tremendously important to your immune system and keeping the rest of your body and mind healthy.

When your good gut flora is damaged or reduced (see #3), then all these health-supporting processes falter. The protective lining of the digestive system breaks down and you get “leaky gut syndrome” where undigested molecules of proteins and other foods get through the intestinal wall into your bloodstream. They are not supposed to be there, so your body mounts an attack. You end up with inflammation (not good, and a big player in many, many health problems), auto-immune conditions, and allergies.

Here’s a list of some of the health problems related to having unhealthy, unbalanced gut flora:

I don’t know for sure, because I’m not a research scientist, but I am going to guess that people with Alzheimer’s could easily be people with disrupted gut flora who have had it for many years.

Okay, enough of the scary stuff. Let’s move on to…

3) What interferes with healthy gut flora?

Antibiotics – the penicillin group are especially problematic for people who are prone to IBS because they allow bacteria from the bowel to move into the small intestine which can lead to IBS symptoms. Dr. Natasha Campbell-McBride says: “Antibiotics change bacteria, virus and fungi from benign to pathogenic, giving them an ability to invade tissues and cause disease.”

Vaccines, especially those containing Thimerosal, a mercury-based preservative commonly used in vaccines. Apparently it has been phased out of most vaccines in North America and Europe with the exception of the flu vaccine.

Sugary, high-carbohydrate foods. These promote the overgrowth of fungi, particularly Candida, as well as bad bacteria, worms, and parasites

High fibre grains. These are very harsh on the sensitive digestive system because they are so hard to break down. Apparently they predispose you to IBS and lead to nutritional deficiencies.

If you’ve had IBS from an early age, it’s possible that you’ve had gut damage and unhealthy flora since birth. You got this from Mum and Dad, but don’t blame them. Many of us come from generations of people with abnormal gut flora, so it all gets passed down the line. Mum and Dad have toxicity from their own parents that wasn’t cleared up. Add environmental toxins and processed foods to that, and you have the recipe for intestinal disaster. We have had an explosion of processed foods and environmental toxins after World War II – so if you were born after that, you have received a much bigger dose than people who were born prior to that tipping point.

I believe this is why you can talk to people in their 70’s and 80’s who say they eat whatever they want and never have a problem. Things were different back when they were developing their digestive and immune systems! (Yet skyrocketing rates of Alzheimer’s and dementia suggest that older people need to rebalance their gut flora, too.)

Although it was once believed that the placenta protected the fetus from toxins in the mum, science now knows this is not true. The baby receives everything the mum ingests or puts on her skin (which is, of course, why there is such a thing as fetal alcohol syndrome or crack babies.) Note to moms-to-be: Do NOT use hair dye, which is the most unregulated beauty product, at least until after you have had your children.

4) How to support gut flora so it fosters your health instead of making you sick.

1. First of all, avoid the stuff in #3 above as much as possible. Please note that, when you stop using and ingesting some of these toxic substances, you may feel worse temporarily before you feel better. This is because the bad flora in your gut starts to die off, which can be uncomfortable, but you definitely want to get rid of it!

2. Detoxify:

Detoxify your home environment by choosing unscented and natural personal care products, household cleaners and laundry products. Remember, your body is not a closed system. Just because something is outside of your skin doesn’t mean it won’t end up inside you.

Throw out the fabric softener (yes, the liquid for the washer AND the dryer sheets) and stop over-drying your clothes if they have static cling. Or wear natural fibers. Everyone we’ve worked with who has bowel problems has reacted badly to fabric softener.

Drink, cook, and brush your teeth with good quality water. If your water is chlorinated, get a chlorine filter or put your water in a pitcher and let it stand for an hour to evaporate the chlorine. Avoid fluoride in water and toothpaste. Sodium fluoride is a controversial substance linked to constipation, diarrhea, nausea, and many other symptoms.

If you need more help with the detoxifying process, you’ll find it in our ebook, Treatment of Irritable Bowel Syndrome, in the No IBS Program, and in our hard copy book, How to Stay Healthy and still Eat Chocolate (the first two are on our Products page, the last one you’ll need to email me about.)

3. Food for good gut flora.

This is almost too big a topic for this blog post, so I am going to summarize.

So far, the best diet I’ve seen for healing gut flora and restoring the lining of the digestive system and the integrity of the walls of the intestines is the GAPS diet.

It was developed by Dr. Natasha Campbell-McBride, who is a medical doctor and has advanced degrees in neurology and nutrition. She has also worked personally with hundreds of patients with serious gut flora abnormalities (and consequent health and brain problems) and helped them to restore their health and get their lives back on track.

If you want to know what to eat in detail, do yourself a favour and grab a copy of her book, Gut and Psychology Syndrome.

In brief, the foods to avoid because they feed the bad micro-organisms are the following (and, by the way, when you have an overgrowth of the baddies in your system, you will crave these foods like crazy!). Some of these foods must be avoided because they are tremendously hard to digest and damage your digestive system (e.g. complex carbohydrates.)

All sweets, containing any kind of sweetener whatsoever. Sweets feed Candida yeast. Artificial sweeteners should be avoided because they are linked to some very negative health consequences including digestive problems.

Soda pop

Alcohol (feeds Candida and is hard on your liver when you are trying to detoxify. Once your digestion is healed, you may tolerate a dry wine or a plain liquor such as vodka, scotch or gin – no fancy cocktails which are usually full of sugar.)

Processed foods. Your body needs the nutrition of real food, not manufactured substitutes that have had one or two vitamins added back in.

Regular milk, yogurt, and cheeses from conventionally-farmed animals.

Regular table salt.

So what does that leave you with?

Helpful foods:

Meat, fish, poultry, eggs. If you have trouble digesting meats initially, make meat or fish broths and stews. These will soothe inflammation in the gut and provide the nutrients that help restore the lining of the gut. People with diarrhea may have trouble with animal fats, so proceed slowly and/or be sure to eat some soluble fibre vegetables such as carrots, beets, pumpkin, or squash at the beginning of your meal to help pre-condition the bowel.

Raw or organic pasteurized milk made into home-made yogurt or kefir. Fermenting the pasteurized milk into yogurt and kefir makes it alive again and is helpful to people with diarrhea, though not necessarily those with constipation. The reason for making your own is because store-bought yogurt is not fermented long enough to provide enough active good bacteria to help restore your gut flora.

Fermented vegetables such as sauerkraut. These work better for people with constipation than yogurt and kefir (although you may be okay with organic butter.) To begin with, have a spoonful of sauerkraut juice daily. You may not be able to tolerate the sauerkraut or other fermented veg until your digestion has had time to heal. These fermented foods help to repopulate the good flora in your gut.

Cooked non-starchy vegetables. Once digestion is healed, raw vegetables can be added.

Ripe fruit, unless you have diarrhea. Once diarrhea settles, start with cooked fruit and move on to raw fruit, especially berries. Do not combine fruit with meat as it interferes with protein digestion.

Sea salt.

Nuts and seeds, unless you have diarrhea. Nuts and seeds can be made more digestible by soaking for 24 hours in lightly salted water (use sea salt only) and drying in your oven or dehydrator at a low temperature.

These are the basics. There is more to know about eating to enhance gut flora, especially in terms of food preparation, meal planning, and the best way to introduce foods slowly to your system, but I cannot possibly cover it all in this article.

4. Supplements to support gut flora.

Dr. James LaValle suggests the following supplements to help the digestive tract recover, rebalance flora, and help to reduce unfriendly flora. I do not know whether or not your body will tolerate these supplements, so please be cautious. If you can be tested to see if they agree with you with a method such as electro-dermal testing, applied kinesiology or dowsing, please do so before using anything here. I’m not a doctor, so these are not my recommendations; I’m just telling you what Dr LaValle says.

1. He suggests rotating (i.e. taking on alternate days) the following three, which have several properties including being anti-fungal, anti-bacterial, and anti-parasitic:

Grapefruit seed extract – along with other good qualities, helps to inhibit H pylori.

When I took these, they made me very tired, probably because of the die-off of the bad micro-organisms in my system, so I decided to take them at night before bed when I was going to sleep anyway.

2. A broad range digestive enzyme (i.e. one containing a wide range of enzymes. You need more than a simple papaya enzyme.)

3. L- Glutamine – an amino acid that helps to repair the lining of the gastrointestinal system. When you have leaky gut, the colon loses a lot of L-Glutamine and you need to replace it. If you buy it in a powder or in capsules containing powder, you can mix the powder into water and drink it, which you may find makes it more bio-available than taking a tablet or hard pill.

Apparently L-Glutamine is especially important for people who are taking chemotherapy as chemo is very hard on the intestinal lining.

4. Sea Cure – helps repair tissues and heal wounds. Reduces inflammation in the colon. (Even though, technically, the colon is not inflamed with IBS the way it is with Crohn’s and Colitis, if you have unbalanced gut flora, the chance of some kind of inflammation is high.)

5. Dairy-free probiotics containing Lactobacillus acidophilus and Bifidobacterium bifidum. Unfortunately, not all probiotics are created equal and many do not contain what they say on the label, so this is where you really have to do your research.

6. Soluble fibre; ground flax seed; rice protein powder.These three help to bind toxins in your digestive system and get them out of you! Try to buy organic versions so you are not adding more toxins to your body in the form of whatever pesticides and fertilizers are used on conventional crops (especially important with rice.)

So that’s it. I know there’s a lot of information in this post, so don’t feel you have to do everything at once. If you have many changes to make to help your gut flora, any step you take in the right direction is a good one. Maybe start with changing your personal care and laundry products to unscented and non-toxic ones, avoiding sweets, and taking some L-Glutamine. Then move on from there.

More help for IBS from the authors...

Hi. We are Karen Alison and Kathy Raymond and we help people self-heal their IBS naturally, with a doctor-recommended method that addresses the least-recognized aspect of this hellish condition – the way the brain triggers uncontrollable symptoms in the gut.

IBS is a lot like having PTSD (also once believed to be untreatable) because of the way your autonomic nervous system is triggered to produce symptoms. But, in a few short sessions, you can learn how to retrain your brain so you shut down the neural pathways that lead straight to diarrhea, constipation, bloating, gas, and anxiety.

If you don’t deal with this underlying root cause of your problem, you’ll have to spend the rest of your life at the mercy of your Irritable Bowel… and it usually gets worse.

But you can make it stop NOW. Just click on this link for more information and follow the instructions to access the program.

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Comments (20)

Hi Joan,
Muscle testing or applied kinesiology is hard to describe in words. The easiest thing for you to do would probably be to look it up on Youtube so you can see a demonstration. Sorry, I don't know a specific video to send you to.

Hi Karen,
Thank you for such an informative response, I really appreciate that.
I take 1 tsp of ACV in half a cup of warm water, can't take it straight, it is too strong.
What is muscle test, and how to do it?

As I understand it, raw ACV is prebiotic (food of probiotics), not an actual probiotic. If the organic, raw stuff helps your stomach acid and helps with gas, it sounds like a useful food. I...

Hi Joan,
Thank you so much for the huge compliment!

As I understand it, raw ACV is prebiotic (food of probiotics), not an actual probiotic. If the organic, raw stuff helps your stomach acid and helps with gas, it sounds like a useful food. I have read, though, that it's best to take it diluted in water as the straight stuff can burn your esophagus.

Miso? Don't know anything about it as a probiotic. It is soy and I am always suspicious of soy for people with IBS as it is generally a poorly-tolerated food even when fermented. Personally, I like the old standbys - a good quality probiotic capsule and some organic, traditionally-made (in brine) sauerkraut. I'm also investigating kombucha as it has an excellent reputation.

Kimchi is another classic probiotic food, used for centuries in Asian cultures (as no doubt you know.) If you tolerate the spice, why not eat it spicy? Not everyone does, but you'll have to make that call yourself. Just make sure it's the real thing, made with brine, not vinegar.

My beef with most vinegars is that vinegar is a challenging food that can feed the pathogenic yeasts etc in the gut and cause more gas and bloating. Nobody with IBS needs more of that. When Kathy and I worked in a natural health clinic, whenever we desensitized people for candida, we always had them avoid vinegar and related foods. Perhaps quality makes a difference. Most vinegars are strained of the mother so lack the potential benefits of the raw stuff.

Hi Karen, I found your website while searching for "how to do Tapping" on youtube. It is the best website I have ever visited about IBS. I have some questions about repopulating gut flora. Is miso (organic one) effective? How about organic...

Hi Karen, I found your website while searching for "how to do Tapping" on youtube. It is the best website I have ever visited about IBS. I have some questions about repopulating gut flora. Is miso (organic one) effective? How about organic apple cider vinegar (ACV), the one with the mother such as Bragg's? In your article you mentioned vinegar is not good for IBS. My Naturopathic doctor recommended I take ACV before lunch and dinner to get the acid. I don't have C or D, I just have this bloating problem and pain. The ACV will help keep things moving and I am able to pass the gas.
Kimchi is spicy, isi it good for repopulating gut flora? There is plain kimchi, it is called mul kimchi, which means water kimchi, but I don't like the tase.
Thank you for such a wonderful and informative website.

Hi Naomi,
That is a great question. The fermented food question is a bit confusing but I think it's because there are two categories of fermented foods.

On one side, you have ferments like wine, beer, alcohol, soy sauce, and vinegar which are...

Hi Naomi,
That is a great question. The fermented food question is a bit confusing but I think it's because there are two categories of fermented foods.

On one side, you have ferments like wine, beer, alcohol, soy sauce, and vinegar which are typically fermented with sugar. They are not probiotic. These tend to feed Candida yeast and pathogens in your gut.

Then there are ferments that are probiotic such as yogurt, kefir, sauerkraut and kimchi. Yogurt and kefir use a "culture" to ferment them (basically a bacterial process) and fermented veggies use salt or brine.

So I guess it would make more sense to call them probiotic foods instead of fermented foods.

Anyway, should you eat fermented foods? Well, we should probably all eat probiotic foods as people have throughout history to support health. But start slowly - you want to ease yourself into it and give your body a chance to adapt, because good, non-pasteurized probiotic foods will help to kill off or crowd out the pathogenic microbes and that can cause a bit of distress in your intestines.

Also, if you eat a lot of sugar and refined carbohydrates, that will feed the bad microbes and cause some explosions when you add probiotics.

Hi Karen, I am just starting out on the crazy and most of the time very confusing journey of trying to get my life long IBS/yeast intolerance (which I'm guessing is linked to candida although haven't been told out right) situations sorted. You're...

Hi Karen, I am just starting out on the crazy and most of the time very confusing journey of trying to get my life long IBS/yeast intolerance (which I'm guessing is linked to candida although haven't been told out right) situations sorted. You're article is so informative and easy to understand. I just have one question, you mention in your article that fermented foods are bad for IBS. However in another part of your article (and which seems to be the premise of the G.A.P.S diet) it is stated that some fermented foods are amazing at re populating your gut with good flora, such as fermented veg like sauerkraut/kimchi, kifir etc are good. I'm finding this issue a bit confusing. Should I eat fermented food? And if so which are the best types. I am also dairy intollerant, so does this mean that I should avoid kifir? Sorry if this is a bit long winded.

Hi John,
Thanks so much for your comment and your kind words!
One thing Kathy and I have found with IBS is that EFT tapping - a form of acupressure tapping - can often help with symptoms and with the stresses that can underlie the condition....

Hi John,
Thanks so much for your comment and your kind words!
One thing Kathy and I have found with IBS is that EFT tapping - a form of acupressure tapping - can often help with symptoms and with the stresses that can underlie the condition. Diet is important, reducing chemical exposure is important, but so is reducing stress levels and dealing with undischarged trauma from the past that may have triggered the nervous system into reacting with digestive issues.

HI Kathy & Karen
This blog is very informative and has given me new ideas. My Doctor thought I had H.Pylori which, was found to be negative. However still undergoing tests with Consultant for Stomach problems. I have changed my diet and only...

HI Kathy & Karen
This blog is very informative and has given me new ideas. My Doctor thought I had H.Pylori which, was found to be negative. However still undergoing tests with Consultant for Stomach problems. I have changed my diet and only eat natural foods, lots of berries all food gluten free which is a bit hard to find no yeast or breads. So it is out with any processed foods and chemicals, cheeses anything I feel harmful. I feel a lot better for it although problem still occurs but no way as bad as it was.
IBS I still have to contend with and also erosive gastritis in which the Doctors think is due to Medications for Spinal problem and Fibromyalgia. I will stay on this Diet as it does help. I read all your emails and blogs and find them very helpful. My best to all of you and stay well.
Regards John

Oregano oil and caprylic acid are great anti-fungals and are often used by people who have an overgrowth of Candida yeast. One caveat is that not all products work well for all people. (Caprylic acid did nothing for me, but olive leaf...

Hi Adam,

Oregano oil and caprylic acid are great anti-fungals and are often used by people who have an overgrowth of Candida yeast. One caveat is that not all products work well for all people. (Caprylic acid did nothing for me, but olive leaf was great.) If you know how to muscle test, you can check the product on yourself in the store before you buy it.

The other thing is to go slowly when you start taking them. These antifungals kill the bad bacteria and that die-off can make you feel a bit sick. It helps if your diet is already fairly clean - no sugar or fermented foods like vinegar or alcohol - they will definitely make you feel worse while you're taking those supplements.